NCIS meets SHIELD
by Rubyrach11
Summary: Gibbs and his team are busy working a case when they come across someone unexpected. What do they have to do with the case? Why is SHIELD involved? Can Gibbs protect his team?
1. Chapter 1

NCIS meets SHIELD c1

Gibbs and his team are busy working a case when they come across someone unexpected. What do they have to do with the case? Why is SHIELD involved? Can Gibbs protect his team?

….

Ellie was in the elevator heading up to the office her thoughts stuck on her family as George had rang her this morning asking her if she had heard from Sam, she hadn't and when she tried to her phone went straight to voicemail. She was officially concerned; maybe she could get McGee to ping her phone. The doors opened and she walked into the ballpein nodding her head to McGee and Torez in greeting. Placing her bag next to her desk she sat down deep in thought.

"You good?" Nick asked coming over to her leaning on her desk looking down at her.

"Huh?"

"You're away with the fairies, what's up with you?" he asked

"Just thinking. Where is Gibbs?"

"Upstairs with Vance. You sure you're good?"

"Family drama." Ellie shrugged

"You want to talk about it?" McGee asked from his desk across from her.

"We can't get in contact with our sister."

"Wait a minute you have a sister?"

"Not the issue."

"I'm with Torez on this, you never mentioned a sister." McGee stated

"Yeah I mean we met your brothers." Torez added looking at McGee for support he nodded his head in agreement.

"Still not the issue." Ellie rebutted

"Does she usually not stay in contact? How long has it been since you tried getting in contact."

"I only tried this morning but my family have tried for two weeks now, she should have gotten in contact by now."

"What's her number? You want me to…"McGee suggested pointing to the computer this made Ellie smile but she refused his offer.

"She travels a lot so she might not have reception."

"What does your sister do?"

"She is a pilot." Ellie replied

"Does she usually stay in contact?"

"I'm sure she is fine." Torez states after McGee.

"You're probably right…"

"Grab your gear." Gibbs instructed coming down the stairs so the team jumped into action as they grabbed their gear Gibbs grabbed his own before leading them to the elevator after explaining they were heading to a dead Petty Officer.

At the crime scene the team got right to it Bishop was taking photos as McGee was taking witness statements Gibbs was with Palmer as he examined the body. Torez was looking around the crime scene that was an alley way before moving over to Gibbs, he winces seeing the body he was obviously tortured before death. The name of the Petty Officer was Clark Boyle so Gibbs sent Torez and Bishop to his apartment after McGee found out where it was as McGee and Gibbs would head abck to the Navy Yard now that Palmer was finished and they have taken the evidence they have found for Abbey to go over.

Ellie was driving to the apartment when she got out and followed Torez up to the entrance of the apartment she found his silence eerie, by now he should have made at least one complaint or observation.

"Is something on your mind?" she asked

"What? Why?"

"By now you would have talked my ear off, or made some strange and irrelevant comment and you have been quiet this whole way."

"Me I thought I'd be nice and leave you with your thoughts. I can tell something is on your mind as you have the crease on your forehead right here." He replied pointing to his own forehead.

"Sorry, just edgy you ready to enter?" she asked as they were outside the door to his apartment. Torez nodded using the keys they grabbed from his body. They entered his room that was sparse with only the essentials, given they were expensive looking essentials.

"Wow this looks like a bachelor pad to me." Torez stated seeing no decorations but had a couch facing a flat screen tv. Bishop looked around the kitchen that was very clean she opened the fridge and saw beer.

"The only thing in the fridge is beer and barbeque sauce." Ellie told Torez before moving into the bedroom they began their thorough search of his home. "No computer."

"No phone." Torez added

"But he has a flat screen tv, surround system, xbox and nothing seems to be disturbed by the looks." Ellie stated

"I agree except the photo." Torez confirmed sitting down on the couch. "This is a nice couch." He added patting the cushions.

"What photo? There are no photos in this place."

"Well there used to be, there is a marking on the table by his bed a clear line where a photo used to be." Torez stated before sighing as he followed Bishop back into the bedroom where he pointed out the mark and she agrees it looked like a photo used to be there.

"We need to find his computer." Ellie stated

"Let's get back to the Navy Yard." Torez led the way out of the bedroom and was about to open the door when Ellie stopped him moving over to the centre bench she knelt down and pulled out her knife. "Hey what are you doing?" But she didn't respond in words instead she dug into the floor board with her knife and a loose floor board came up. "Oh wow." Torez exclaimed as he moved towards her.

"Our Petty Officer was into something shady alright." Ellie agreed as she pulled out her camera documenting what she found as she then pulled out a duffel bag full of money.

Back at the Navy Yard they briefed Gibbs on what they had found they were then sent off to go and talk to his ship mates and crew as Gibbs would take McGee to talk with his CO. Bishop has spoken to four of his ship mates before moving over to Torez he was just finishing up his latest interview.

"What did you get?" She asked

"As far as I can tell he seemed like a decent man he worked hard I was surprised to hear he had a girlfriend." He stated

"Me too, they have been going out for three months, that was when he changed became more serious less childish more nice."

"Did you get a name?"

"Yeah Sam, one of his friends had met her and I have a basic description brown hair blue eyes my height but he said she seemed smaller and no last name. I gave him my card if he can think of anything else we should keep going." Ellie stated moving on to talk to more of the crew. They were there for over an hour getting statements when they finally finished they headed back to the Navy Yard.

"We got a ping on his phone." McGee greeted them as they entered the ballpein so they turned around heading to the address that Tim had found. It was an industrial area where they fanned out searching for his phone. Ellie froze as she waited for Torez he came up behind her and saw her posture.

"Everything okay?" he asked

"This place is giving me the creeps. Do you feel as though we are being watched?" she asked

"No this place is large and empty except for us, you are right this place is creepy." Torez states looking around him to make sure no one was watching them. They searched the building it was Gibbs that located the phone but it had been stepped on and smashed. They returned to the Navy Yard where McGee went to go and work with Abbey trying to get anything off the phone and Gibbs went down to the morgue to talk with Palmer. Torez sat down at his desk looking at Bishop who was watching her computer screen.

"I swear if you ask me again if I am alright I might shoot you." she stated before he could ask so instead he shrugged returning to his own paperwork. "I'm going to go down and see if Abbey needs help." Ellie said leaving the ballpein heading to Abbey's lab.

The next day Ellie entered the ballpein looking around the room she didn't see any of the others, she checked her phone but found no text messages. So she got herself comfy at her desk pulling out her laptop she started trying to piece together a timeline for Petty Officer Boyle.

"Morning Bishop did you hear?"

"No what?"

"We found his girlfriend. Gibbs is in the interrogation now talking with her."

"Oh, where is Nick?" She asked McGee

"He is with Gibbs." He said moving towards the interrogation room, she got up and followed him into the observation room. She was surprised Jack was already there watching as Gibbs sat across from a girl with her head tilted down all Bishop could see was brown hair.

"Hey what have we missed?" Tim asked

"She hasn't looked up since entering the room, Gibbs has just been sitting there. Nick is in the corner. It might be best if Ellie swaps him out though."

"What me? Why?" she asked

"Well considering the state she was in when Gibbs found her, it looks like she has been beaten. It might be easier to have a female face."

"Then you should go."

"I need to observe from out here."

"You going to talk to me?" Gibbs finally asked breaking his silence. "Tell me about Petty Officer Clark Boyle." Gibbs tried

"He's dead." She replied breaking her own silence without looking up.

"How did you get those bruises?" Gibbs asked, this was when she finally looked up and Ellie gasped Tim looked at her then back at the girl across from Gibbs, the left side of her face was purple blue and she had a split lip it obviously wasn't from walking into a pole. Ellie left the observation room and entered the interrogation room Gibbs and Torez looked over at her both curious as to what she was doing. But she wasn't looking at her boss or her friend she was tuned onto the brunette sitting down at the table not looking at her.

"Sam?"

"Bishop?"

"Sam what the hell?" Ellie asked not answering Gibbs.

"Hey El long time no see." Sam finally turned to look at Ellie which had Ellie knelling in front of her checking over her face.

"What the… Who did this to you?"

"Doesn't concern you. Why am I here?" she asked looking down fiddling with her sleeve. This had Ellie looking at Gibbs who was looking at her waiting for her to answer his question.

"Of course this concerns me you're my sister." Ellie stated focusing on her sister not her boss or friend.


	2. Chapter 2

NCIS meets SHIELD c2

"Why am I here?" she asked again, this time before she got to answer Gibbs was pulling her out of the room out into the hallway.

"Explain." He stated

"It's Sam my younger sister, Gibbs I had no idea she was in DC. This makes no sense." Ellie replied

"Why?" Gibbs asked noting that look in Ellie's eyes meaning she was thinking something over that usually leads to something important.

"Let me talk to her." Ellie asked and after a small hesitation he nodded and watched as she re-entered the room giving Nick a signal he left the room closing the door behind him. Sam was watching her and Ellie couldn't help looking over the bruising and cut lip but her sister's eyes were the same the unwavering blue as she looked at her. "You need to talk to me Sam, I can't help you if you don't talk to me." She stated but she saw the determination in her eyes and her closing up once again.

"Why am I here?" she asked again.

"What do you know about Clark Doyle?" she asked

"He's dead." Sam replied straight faced. "Why are you asking me about a dead man?"

"He was murdered." Ellie replied carefully. "How did you know him?"

"We went out."

"How long?" she asked

"A while." Sam shrugged

"Do you know where his computer is?"

"No."

"Did you stay at his place?"

"A few times."

"We know you have been dating at least three months, talk to me please?"

"Ask me what you really want to."

"Do you know who would have wanted him dead?" Ellie asked that was when she saw it, in her sister's eyes she was shutting her out. "Sam?"

"What do you want from me El? Clark is dead it doesn't matter now." She replied

"We can get him justice." She stated but Sam turned her back on her she placed her hand on her head as she brought her legs up to her chest before resting her forehead on her knees. The door opened and Ellie turned to see Jack enter the room she came and sat next to Ellie looking at Sam carefully.

"You know who killed him? Don't you?" Jack asked this time Sam did look up from her spot tilting her head so she was looking at them. There was something in her eyes that had Jack on edge, she saw it when it was just her and Gibbs but she saw a complete change in attitude when Ellie entered the room but now she was seeing that same spark from earlier return. Just then the door opened once again both Jack and Ellie were surprised to see an unfamiliar blonde enter the room holding a brief case.

"Natalie Jones, Miss Bishop's lawyer. You have no right to question my client without her council present. Now if you don't mind I would like to talk to my client in privacy. You can empty the observation room and turn off all the recordings." Natalie Jones stated Ellie was in shook, Gibbs was fuming Jack was surprised so was Sam but she recovered more quickly but Jack noticed it. When the room was clear Sam looked up at the blonde who was standing in front of her.

"I don't recall calling a lawyer." Sam stated

"Maria sent me."

"Of course she did."

"She thought you needed back up considering who is on this team."

"I was doing fine."

"We can pull you out."

"I need to know what they know. You may want to get yourself comfy you are committed now." Sam said indicating for her to sit down next to her. This time Ellie didn't re-enter the room it was Gibbs and Jack they sat across from them.

"Is my client being charged with something?"

"Not yet, it depends if she intends on obstructing a federal investigation." Gibbs replied

"Ask away." Sam stated as Gibbs then opened the file bringing out pictures of Clark's dead body, Sam looked down before looking up at Gibbs.

"Most people who have been in a relationship for three moths seem to get some form of reaction teary or disgust."

"I'm not most people. You want me to shed a tear for a dead man? What is the point?"

"Grief?" Jack stated as Gibbs started bringing out more pictures of Clark's apartment.

"You were going out for three months but there was nothing there to indicate you stepped foot in his apartment." Gibbs stated this got a reaction from Sam as she turned to her lawyer looking at her expectantly her response was the slightest shake of her head.

"There should have been…there is that barbeque sauce is mine." Seeing the photo of the fridge. "It is not like we spent a lot of time there from him being stationed we mainly spent our time in the bedroom."

"Sam." Natalie warned

"No, where is Ellie?" she asked looking at Gibbs

"She is busy. You have me!" Gibbs replied as Sam looked at the mirror behind Gibbs Ellie who was standing next to Nick and Vance watched as her sister was being interrogated by Gibbs.

"Freaky it's like she is starring right at you." Nick told her as he spoke Sam turned to look at him and he yelped. "She can't see me right." He stated seeing Sam's eyes and how they held an anger in them. Ellie sighed once again being the focus of her sister's attention through the glass.

"Just ask me what you want to ask me." Sam finally stated not looking at him.

"Did you have anything to do with Petty Officer Clark Doyle's death?"

"No." Sam stated finally looking at Gibbs and he had to swallow seeing the look in her eyes. Jack was watching this scenario closely she could see the anger building up in the younger Bishop's eyes.

"Do you know where this came from?" Gibbs asked showing a picture of the bag full of money, Jack noted how this seemed to get her attention.

"How much?" Sam asked surprising everyone as that was not the typical answer they were expecting.

"Half a million." Gibbs replied hardening his glare Sam held his gaze without falter she knocked the table as she moved in the chair that was when her lawyer intervened

"She has answered all your questions. Are you charging her?" she asked

"Not yet…" before he could continue both the lawyer and Sam were standing up.

"Then we are leaving. If you want to contact my client again." Natalie hand placed a piece of paper on the table before walking Sam out of the room. Gibbs turned to look at Jack but she was up following them out to the elevator. The two women didn't talk, they stood in silence as they waited for the elevator. Ellie came running out after them side stepping Tim and Nick and standing next to Jack.

"Sam where are you going?" she asked her sister turned to look at her Jack noticed the flash of pain across Sam's eyes but then they hardened.

"I don't know you, leave me alone." Sam stated before getting on the elevator with her lawyer and Ellie noted that look in her eyes before the door closed they were pleading with her but she didn't know why. Ellie moved to the door pressing the button wanting it to come back up.

"Ellie, we need to talk." Jack stated

"Not now."

"Yes now, come with me." Jack said taking Ellie up to her office much to Ellie's protests.


	3. Chapter 3

NCIS meets SHIELD c3

 **AN: warning there is mention of violence in this chapter.**

"I need to get after her, I think she is in trouble. Why wouldn't she talk to me…" Ellie started as they got into Jacks office.

"I need you to tell me everything about Sam."

"I need to get after her." Ellie began but Jack silenced her holding up her hand.

"You need to tell me everything about Sam." Jack repeated Ellie looked at her about to argue but Jack had a certain look in her eyes that had her halting her arguments. So she spent an hour in Jacks office.

Torez was tailing Sam Bishop and her lawyer they were in a black sedan driving for half an hour before pulling over at a diner entering the diner Torez pulled over and waited in the car. 10 minutes passed and he couldn't see them so following a hunch he entered the diner he didn't see them anywhere swearing silently he went to the back door entering the alleyway he looked around but didn't see them. He started down the alley shaking his head, he had no idea where they went to. Pulling out his phone he dialled the number dreading this phone call he called Gibbs.

Gibbs was at his desk waiting for Bishop to finish with Jack, he had just gotten the call from Torez stating he had lost her. He was not happy about that so he called him back here, McGee was working with Abbey in the lab so he decided to head down there to see if they had found anything. He was stumped by Ellie's sister, her reactions to what was happening had him suspicious of her especially with her reaction over the money what was she up to?

"What have you got?" Gibbs asked entering the lab to see McGee and Abbey working at the computer. Abbey looked up to him and smiled as he came in, it being clear that McGee had informed her of everything that has happened.

"You can't think Ellie's sister had anything to do with this? Do you?" Abbey asked

"She is hiding something, now what have you got?" he asked again

"Sorry right, well we have a partial running and maspec is running some substance that Jimmy had found on the body. Other than that we managed to get some of the data from his phone, it looks like someone tried to erase it before the smashed it."

"You found something?"

"Yep…" she said bringing up a picture on the screen this made Gibbs sigh as he leaned in trying to identify what was in the photo. "This is the first one and I have no idea what it is it could be a sculpture of some sort. I had more luck the second one it was badly damaged but I managed to piece it together it was a photo that was received before Jimmy's time of death. This was followed by a message. I couldn't put the message together all I got was this assorted group of numbers. But the photo was this." Abbey stated pulling up a photo, she didn't recognise the person in it but clearly Gibbs and McGee did.

"Don't show this to Ellie." Gibbs stated he kissed her on the check before he started walking off.

"Why? Wait I have more." Abbey said stopping him from exiting as the computer bleeped.

"What else?" Gibbs asked

"It was a video it took longer but it just finished now." She said as she pulled it up, there was footage of the same girl from the photo tapped to a chair the sound was muffled at first Abbey thought it was damage but it turned out the person that was recording it had their hand over the microphone.

' _Tell us why you want it?' A man shouted at the girl in the chair but she didn't respond there was a thump as another man punched her across the face._

' _Tell me what we want to know.' He said again_

' _Go to hell.' The girl replied another slap but the man stepped back on instruction and a new man stepped forward he was holding a cattle prod._

' _Last chance.' The first man stated but she spat at him and was rewarded with the prod to the ribs her fists clenched and she screamed the scream was clear enough. 'Now answer us?' he said but the girl actually started laughing, she was rewarded with two more jolts and a three more punches._

' _You weren't supposed to knock her out we need answers.' A voice to the side stated the punching man came back into view with a bucket, but before he chucked it on her he checked her pulse._

' _Shit, you juiced her too much.' He said cutting one of her hands free that was when things got blurry as the cameraman moved. He then dropped the phone but it was still recording and a lot of crashing noise came next followed by shouts. Before the phone went dark._

"What was that?" Gibbs asked

"Was it sent to his phone or was it recorded on his phone?" McGee asked

"Recorded on his phone." Abbey replied she was still somewhat in shock at what she had seen.

"The footage was blurry can you get any identities?" Gibbs asked

"That is as best as I can clean it up, none of the men actually look at the camera, I could get an id on the girl."

"No need we know who it is. Again don't show this to Ellie, I need to talk with Jack McGee I want you and Torez to find her." Gibbs stated leaving the lab.

"Wait McGee who is that?"

"That is Ellie's sister, looks like she is now a person of interest." McGee stated heading up to the ballpein to Torez leaving Abbey in the lab.

Gibbs knocked on Jack's door she opened the door he was surprised Ellie wasn't there he looked at her with a raised eyebrow.

"She said she was going to try to get in contact with Sam." Jack said inviting him in,

"Abbey has sent you something up." Gibbs stated looking at her expectantly.

"Everything Ellie told me doesn't add up to the person I saw in interrogation. There is something else too. She has a soul mark." Jack stated

"Sure that is rare but what is odd about that?" Gibbs asked

"It was female writing." Jack replied before shifting her gaze to her computer pulling up the file that Abbey had sent her she sat in silence as she watched the video and leaned back in her chair once it was finished thinking over everything she knows.

"I think we need to talk to her again."

"Do you think she killed him? It could have been self-defence." Gibbs stated

"I don't think she is a civilian." Jack stated but looking at Gibbs she could see he already figured that out.

"Torez and McGee are trying to locate her now." Gibbs stated

"Be careful Gibbs she was tortured we have no idea what happened, she didn't exactly look to be in good shape at the beginning of the video."

"You think she was tortured before the video?"

"Looks like it. But why? Why was she tortured? What was the 'it' they were talking about?" Jack replied

"We will just have to ask when we find her." Gibbs replied before heading up to brief the Director he looked as he saw Ellie at her desk on her phone he met Torez's gaze making it clear for him to keep an eye on her before continuing up the stairs. He was in with Vance for ten minutes talking when his phone went off it was from Torez, he was with McGee and they had followed Ellie who was now meeting up with Sam what did he want them to do. Gibbs then left Vance grabbing Jack as he left the Navy Yard heading to the place that Bishop was at. They were at a diner when Gibbs entered with Jack he had Torez and McGee out back in case she tried doing the disappearing act. Torez entered through the back door blocking that exit he moved up closer.

"Gibbs?" Ellie asked confused he didn't sit down he was looking at Sam she was looking up at him and held his gaze.

"You need to come with us." he stated he was a little surprised that she wasn't that surprised to see him there she tilted her head before nodding her head standing up Torez went to take her arm to escort her and she flinched away from his touch she brushed it off and Torez did step back to give her space Jack ended up walking beside her to the car. When they went back to the Navy yard they were back in the interrogation room with Jack and Gibbs.

 **AN: so what do you think? I like to hear your thoughts until next time.**


	4. Chapter 4

NCIS meets SHIELD c4

"Is there anything you want to tell us?" Gibbs asked, the whole ride back she sat in silence.

"What do you want to know?" Sam asked

"Who do you work for?" Gibbs asked

"I'm a pilot," Sam replied

"I don't believe you." Gibbs stated

"Believe what you want Agent Gibbs I am a pilot."

"We recovered Clark's phone, it was pretty damaged but we managed to recover some off it."

"OK? What does that have to do with me?" Sam asked but he saw it in her eyes she knew where this was going.

"I asked you did you have anything to do with Clark Doyle's death." Gibbs stated

"I told you no, I didn't."

"I don't like being played or lied to."

"I haven't lied." Sam rebutted and that was when Gibbs started the video, she just sat there he was watching her. "Your point?" she asked after it finished

"This was recorded on his phone, you somehow got out."

"You have no idea what happened."

"Then tell us." Jack stated she could see Sam was getting worked up.

"You have no idea what is going on, you are so out of your depth…"

"You need to calm down."

"I am calm…" Sam stopped she stood up the chair falling backwards as she did, she stumbled as she reached the wall. Gibbs and Jack got up both concerned but she held up her hand stopping them from coming closer to her. She gasped holding her hand to her shoulder looking down before looking up. "Worse possible timing." She muttered to herself before looking at Gibbs. "I need a phone." Jack handed her phone it being clear something was wrong Gibbs froze as he recognised that look.

"Your soulmate?" he asked Sam met his gaze before gasping again she pressed up against the wall sliding down to the floor. He hands were shaking as she dialled the number, it went straight to voicemail. Cursing she dialled another number.

'Sierra…alpha…bravo185.' Sam stated into the phone … "Come on… thank god Maria, Nat you need to get Nat help." She practically shouted in the phone… "Nat first, please…I'm heading to her now." Sam said getting herself up she moved to the door opening it then heading out she was surprised no one was stopping her but right now she wasn't focused on them. Instead of waiting for the elevator she took the stairs practically jumping down them.

Gibbs followed her as did Ellie she was very confused chasing her sister down the stairs. Several agents looked up in the lobby as she ran through but when they realised agent Gibbs was with her they let her be one thought Gibbs was wanting to stop her he ended up on the ground. She jumped in the first car she found planning to hotwire the car but was surprised when Gibbs handed her the keys. She didn't question it, she didn't even protest to Gibbs and Ellie climbing in the car. She drove fast, ignoring the curses from her sister in the back seat, Gibbs was holding onto the door tightly as she missed several other cars. He was surprised she missed them all, not one car did she hit. She drove to Norfolk surprising Gibbs even more, but he became concerned when they were waved in through security by men clearly not military. They were in black cavalla and armed with semi-automatic guns. Sam pulled up to four SUV's jumping out of the car as it came to a stop moving to the men in black who were waiting for her.

"Andrews you are to keep her here. You hear me she follows it is on you." Sam stated indicating Ellie who was protesting, Andrew nodded his head moving over to Ellie Sam then moved over to the centre car stopping in her tracks.

"Steve?" She asked, she was very confused as to why he was here.

"Sam, here." He said handing her a vest which she put on and taking a hand gun.

"1 you're with me, two I want a perimeter no one leaves the base."

"Yes Ma'am." They all shouted a group of them split off the remaining me moved in closer.

"You all have had your briefings?" she asked they nodded their heads. "Right you see it you don't touch it, call for containment. Let's move out. Agent Gibbs I take it you are coming?" Sam asked he looked around at the men all of whom were taller than him he nodded his head. Ellie was stuck on looking at Steve.

"What about me?" she asked

"I need you to stay here, I can't focus on you and her." Sam stated and Ellie saw in her eyes she was pleading with her again this time it was obvious what she wanted. So she nodded her head in agreement. Sam placed an earwig in her ear before making the signal to move out the nine men fell into line Steve was walking beside Sam as they took off at a steady jog. Gibbs followed along he was curious at what was going on. She made another signal and two men split off Gibbs watched them leave for a second before he returned his attention to where the others were going. They were heading to a hanger used to station some form of plane. That was when Sam stopped taking cover behind some military jeeps. She made some hand signals and four other men took off two heading in different directions.

"Nat is up there, we need to get up there."

"Do we know if it is there?" One of the men asked Sam held out a device she was given.

"It looks like it is that way." Sam stated "Ruez, Leo take the west entrance (the hanger door) Rodgers, Gibbs and I will take the ladder." Sam instructed four heads nodded. "Remember there may still be military personal in there, only if they threaten you do you engage." Sam stated she knew she didn't have to, these men were experienced and they weren't a strike team for no reason. Sam made the signal for them to go Gibbs was surprised that the ones she called Ruez and Leo entered the truck and began driving up they got close to the building where they pulled away from the truck heading for the ladder heading for the roof.

"Status?"

"Tango1 in position."

"Tango2 in position."

"Tango3 in position."

"Overwatch in position you are in the clear."

"Insert." Sam stated jumping over the last rung and up onto the roof Steve followed her with Gibbs bringing up the rear, they only managed to dive behind a vent before they were greeted by bullets. Sam looked at Steve and held a hand out to him.

"What?" he asked

"You are Captain America." Sam stated to which he sighed before jumping over the vent his shield on his arm he then took out the assailant with his shield that was shooting at them. Sam moved over to where Natasha was tucked away. Sam wasn't surprised she didn't have a weapon to her face when she appeared in front of her.

"You took your time." She stated as her greeting this made Sam smirk that is what she had said to Natasha when they first met.

"Sorry traffic." Sam replied bending down next to her.

"You need to go get the object before they get away."

"We have the base on lockdown." Sam stated

"Then you need to get it before they use it."

"You're hurt." Sam refused

"I'm fine leave me with Ruez and Leo go get them." Natasha grounded out as she moved into a different position.

"Fine, but we will have a talk." Sam said getting up she moved to the edge of the roof holding up the device she scanned the area, Gibbs watched her it looked like she was holding a compass and was trying to find north.

"The Cargo aircraft stationed on the tarmac." Steve suggested Sam was nodding her head in agreement.

"All units the cargo aircraft on tarmac c12." Sam stated over the com unit then jumped off the roof Gibbs moved to the edge shocked but sighed when he saw she landed on the container before moving over to the truck next to the container. Steve looked to Gibbs shaking his head at her, before doing exactly what she did jumping down and running after her as she ran towards the plane that seemed to be getting ready to take off.

"All planes are grounded right?" Sam asked over the coms.

"Yes." Came her reply

"I don't think these guys have got the memo." Sam said picking up her pace she wasn't surprised that Steve easily caught up to her and over took her heading for the plane. "Damn supersoldier." She mumbled but picked up the pace

"What is the plan exactly?" Steve asked

"Stop that plane." Sam replied as she pushed herself to go faster seeming that the plane had started moving rather slowly. "Do something very reckless." She said jumping onto the door as it was closing, rolling inside she jumped up to see six men all dressed in military getup.

She slowly got up smiling at them as they were still in the shocked faze they were strapped to their seats so she knew she had only a few seconds before they got up. She scanned the room saw the box in the centre of the plane that was what this whole assignment was about. Grabbing her gun out of its holster she fired her weapon three times. Steve watched as the plane door sealed shut he was still running trying to think of something he knew Nat would kill him if something happened to Sam that was when he heard a gun fire three times and he shouted out Sam's name. There was a squealing noise and the cargo door opened crashing to the ground one man tumbled off it hitting the tarmac, sparks flew off as the plane continued to drive on. Taking a deep breath he followed Sam's lead jumping up onto the ramp looking up her saw Sam fighting one man as another was coming up behind her. He saw two men already unconscious one man was heading to a box near the front of the plane.

"Sam behind you." Steve warned her in time she dodged the knife aimed for her back the man holding the knife lost his momentum until Sam grabbed his hand and continued on his advance the knife landing in his comrade before the knife wheeler ended with an elbow to his nose blood spurted from it but he sank to the ground unconscious with a well- placed wake. By this time Steve had managed to get up to the last man heading for the box.

"Carful Steve." Sam warned him, she didn't need to he had read the briefing of this particular 084 and knew not to touch it. He managed to get around the man and knocked him out with his shield. "Carry that everywhere?" Sam teased it was a long going point she always seemed to bring it up in a teasing manner since being introduced into the Avenger's family as Natasha's other half.  
Soul mates were rare, very rare and it was said if you had a soul mate you were blessed. He had met Sam on several occasions he liked her and seemed to be perfect for Natasha she found pleasure in making him uncomfortable the way Natasha did but always was nice about it and usually stuck up for him when the others would tease him. "You deal with the piolets. Let's stop this plane." She instructed he nodded in agreement that was when the plane jolted and turned very sharply. Both Steve and Sam were thrown around the plane, to Sam it felt like she was a rag doll that was when she blacked out.

 **AN: Is Sam alright? That was a lot to take in I hope you enjoyed it, tell me your thoughts until next time.**


	5. Chapter 5

NCIS meets SHIELD c5

She woke up not long after coughing slightly there was smoke so she knew they must be a fire somewhere. Her eyes landed on Steve he wasn't that far from her but she was trapped by a piece of reidbar pinning her in place. She looked down at her body she seemed to be in one piece which was good.

"Sam?" Steve was calling her

"Huh?"

"I'm coming Sam." He stated

"No, you need to find the 084, I'm not going anywhere. Find the 084."

"I can get to you." he affirmed

"No, you're going to need some gear to get me out of this. You need to find the 084 get it in containment before anyone touches it." Sam stated

"I will be back."

"I'm not going anywhere." Sam stated trying to free herself only to fail, she would have to wait for help to come get her. It felt like ages before she heard anyone get back on the plane by this point she realised the smoke was getting thicker.

"Hey." Ellie stated with other people Sam didn't recognise

"I see you found yourself in a tighter spot then I was."

"Very funny, I would like to get out." Sam said not amused at her partner's statement over the com in her ear.

"Tango has contained the 084. The Navy has got some equipment to get you out." Natasha replied through the coms.

"You should be on your way to medical." Sam stated

"I wasn't leaving without you." came her reply

"Maria can't you order her back?"

"Think I haven't tried?"

"I thought I told you to wait by the cars?" Sam said turning her attention to her sister.

"Gibbs told me what happened…you have a lot to explain. To start with you know Captain America?"

"Steve? Oh right how am I to explain this…friend of a friend so becomes my friend." Sam stated liking that idea even though the friend she is friends with is more than friends with her but that was another long story.

"What?"

"How am I getting out of here? It's just I have a head ache."

"They were putting out the fires first, we have equipment coming oh look speak and it shall appear." Ellie stated as Marines came in with gear to cut through metal.

"Are you hurt?" Maria asked over the coms.

"I'm fine."

"What was that about a headache?" she asked

"Forgot coms was on, I may have a concussion is all." Sam stated waving her hand if it was no big deal.

"Concussion?" Ellie asked worried for her sister.

"I'm fine but I would really like to get out now." Sam stated

"Working on it." Ellie replied as a Marine came closer to examine the area Sam waved at him he looked down nervously.

"Anyone call for assistance?" a familiar voice crackled across the coms. Sam tilted her head hearing the familiar sound outside followed by the commotion from the onlookers.

"Should I be concerned that you got onto this secure channel?" Sam asked

"What I couldn't let my prodigy die."

"Seriously Tony…firstly I am not your prodigy and secondly I'm not dying."

"Tomato potato." He replied before the metal trapping her glowed orange as he lazered through the metal.

"Wrong analogies." Sam stated but accepted the help when Tony cut her free he held out his hand to which she took always finding it strange touching his armour as he pulled her up and off the plane. Everybody was staring at them or more accurately they were looking at Tony Stark in his iron man suit he had his helmet off but he was still worthy of looking at. Ellie grabbed Sam hugging her tightly after checking over her once she was reassured Sam left the plane with Tony on her heels as she made her way over to where Natasha and Steve were. Steve looked up and smiled at her but noticed she wasn't looking at him so he moved out of her way. Natasha was grumbling and the medic that was trying to look her over but it being obvious he was very nervous around her.

"пусть доктор посмотрит на тебя." Sam stated (let the doctor look over you)

"I taught you Russian you can't lecture me in it."

"You wouldn't listen to me in English." Sam smiled moving next to her

"You let the medics look over you?" Natasha asked

"I only just got out, you have been waiting for me…you could have let him look you over then we could get out of here." Sam retorted

"Case closed?"

"Mostly," Sam said looking at Gibbs who was watching her closely

"Stark." Natasha greeted nodding her head to him giving him a silent thank you he returned the nod before turning to Steve they began talking to each other. Sam saw the other NCIS agents each one watching them with a different reaction. Tim was in awe of Stark, Torez was looking over Steve trying to make himself seem taller. Gibbs was only watching her as was Ellie, Jack was taking everything in the way shrinks do Sam huffed Natasha reached up grabbing her hand and holding it tightly making Sam look back at her.

"ты в порядке?" Natasha asked (You okay?) Sam was eying Natasha she gave her a small smile before squeezing her hand then moved away heading to Director Vance.

"I will meet you back at NCIS for your debriefings." Sam stated and before he could reply she turned on her heel and walked away from them. Helping Natasha up she headed for one of the SUV's with Steve and Stark his armour seemed to disappear but she knew it was in his watches on each wrist. They then drove off the base disappearing from sight.

Gibbs looked around he was stumped he went over to Jack and Vance as they were still looking around there were still plenty of people in the black tactical gear they were instructing the MP's on what to do next and handling the clean-up there was one person in a suit over seeing everything Gibbs had gone over to him to demand an explanation but he was simply shown a badge one he did not recognise but it seemed Vance did and it gave them the right not to answer questions and to take lead. Gibbs was not impressed he turned to Jack hoping for anything from her but she simply shrugged before walking back towards their own cars. Jack hopped in the one Gibbs got in which he was grateful for.

"This explains a lot." Jack stated after several minutes of silence

"DO you know what agency? I did not recognise the symbol."

"I've met them once before, a few years back when I was stationed overseas. They turned up in an instant and were gone just as quick. They took something we had bets going as to what it was we were even joking about how it was alien. They showed that badge took the damn thing we were in quarantine for two days before being able to leave only to be followed by a debriefing that lasted hours. We were simply told never to mention what happened again and all signed nondisclosure agreements… I think Ellie is in shock." She added after a while

"I will talk with her when we return."

"What does this mean for our case?"

"We still need to find his killer, it doesn't look good for Ellie's sister."

"I don't think she did it." Jack stated

"What? Why? She seems capable."

"When you questioned her earlier I believe her that she didn't kill Clark Doyle but I do think something bigger was at play. She has a soul mate so why was she going out with Clark? Where did he get the money? Who were those people on the plane?"

"We will find out in the debriefing."

"You think we will get actual answers?" Jack asked knowing last time she dealt with this organisation she didn't get one straight answer and she found it very annoying that she couldn't get a read on them. "It helps that Ellie will be there." She added

"Why do you say that?" Gibbs asked

"Whenever she was in the room her attitude changed I could actually get a read on her she doesn't want to disappoint her."

"Who was that man in that flying suit?" he aksed

"Tony Stark. Oh come on Gibbs you have to know who Tony Stark is. I wonder how she knows him. Please tell me you recognised the other man."

"Steve Rodgers."

"Yes Captain America he and Tony Stark are part of a group called the Avenger's they protected the Earth from two alien invasions." Jack stated looking at Gibbs as he focused on the road. "I know you don't watch tv or is connected to the internet but you did hear about the battle of New York?"

"Of Course I did I was working that day, it was on every tv in this place." Gibbs huffed the rest of the car ride back was left in silence. When they got back to the Navy Yard and up to the ballpein he was surprised to see Abbey and Jimmy were waiting for them. McGee and Torez went over to them Jack stayed as she was watching Ellie who was sitting at her desk Vance headed up to his office Gibbs looked from McGee and the others to Ellie and Jack focusing on them.

 **AN: hey there what do you think? Will Gibbs get his answers? Did Sam actually kill the Boyle? Find out in the next chapter. Until next time.**


	6. Chapter 6

NCIS meets SHIELD c6

"Back to work we still have a killer to catch." He gruffed making McGee and Torez jump to action they headed to their desks but stopped as the elevator door opened and Sam came out with three other people two of them were in suits the one next to Sam was her soulmate Gibbs didn't catch a name except maybe a nickname Nat? He watched as they strolled through the ballpein as if they owned it none of them even looked at them as they walked past, he did note that the two suits were walking in the front as they walked up the stairs heading for the director's office. Gibbs looked at Jack before getting up and following after the strange agents. When he entered the room he saw Sam leaning against the wall with Nat the two suits were in front of Vance's desk talking with him when he entered they both turned to him and to any other agent he might have found it unnerving at their identical expressions. Jack moved away from him so she was standing next to the wall happy just to observe, she noted how Sam's partner was watching her with an unwavering expression.

"Gibbs we have been asked to assemble in one of our conference rooms. Get your team and meet us at conference room 3." Vance stated but Gibbs didn't move.

"Just who are you?" Gibbs asked

"I am Commander Hill, we will explain everything when you assemble your team. It is best to gather your people it will save us having to repeat ourselves." The female suit lady stated Gibbs glared at her but she held his glare. He begrudgingly complied getting his team all into conference room 3 where they all looked at the agents in the suits waiting for them to begin.

They were in the conference room for three hours listening, arguing and finally settling on an arrangement. Gibbs looked around his team when Commander Hill read them in on what it was the object they had recovered at Norfolk. Several shocked expressions followed by an awkward silence as they digested what it was and how dangerous it was. Ellie was looking at Sam throughout most of the briefing Jack noticed how when Sam did meet Ellie's gaze she would look away almost instantly. She also noticed that her soul mate was watching everyone in the room closely and those times Sam did look at Ellie she would lean in closer to Sam offering support. When the debriefing was finally over Gibbs brought up Clark's death once again.

"What about his death?" Maria asked looking at him.

"We still have our own jobs to do and that is to find his killer." Gibbs stated looking at Sam this time as he said it. He noticed that the woman standing next to Sam tensed she seemed like she was going to step forward but Sam put her hand on her arm stopping her.

"I already told you agent Gibbs I did not kill him."

"We have footage of you fighting men where his phone was."

"Let me remind you I was being tortured there so whatever happened in that room was self-defence and secondly Clark was not part of it."

"His phone says otherwise."

"Just because his phone was there does not mean he was there."

"So you saw everyone in that room?" Gibbs asked

"Yes."

"Where are they then? Who were they?"

"Not a problem anymore."

"What is that supposed to mean?"

"Most of them are detained."

"And the rest?"

"On the run."

"Why don't I believe you?"

"Believe what you want it's the truth."

"Why would you let them get away when they tortured you?" Gibbs asked he again saw the red haired agent tense at his questions but Sam remained completely calm.

"Because we needed them alive. They had something we needed so I didn't kill them."

"Did you get what you needed?" Jack asked she was interested in this conversation she could tell the other SHIELD agents were tense with Gibbs questions but Sam was completely relaxed she was holding Gibbs's gaze as they talked like the others weren't even there.

"That wasn't my job."

"Enough, I will have some agents bring over files on those we obtained. This line of questioning is over. You have all signed the nondisclosure agreements. We will be leaving." Maria stated grabbing everyone's attention Jack noticed that ever since stepping foot in the room Maria was the one in charge giving off a higher authority vibe and she was very good at it. Gibbs found himself losing in a glare off with the Commander he was the one to break away.

Maria now that the documents were in the hands of Agent Shaw she was one of SHIELD's best lawyers Maria led them out of the conference room she noted how Sam seemed to want to stay and talk with her sister but nevertheless she followed them out heading for the elevator. As they walked through the ballpein Sam looked over the row of empty desks her gaze landed on their M.E. and Scientist who watched them, they both seemed surprised but her gaze continued over them until she was looking at Maria once again. Her heart rate had picked up and anyone looking at her wouldn't see a change in attitude but Maria and Natasha both knew her very well and instantly could tell something was wrong. Director Vance had followed them out as did Gibbs and his team.

 **AN: this chapter was shorter just to cover the debrief, what made Sam go on high alert? Find out next time until then check out my other stories.**


	7. Chapter 7

NCIS meets SHIELD c7

Director Vance had followed them out as did Gibbs and his team.

"Agent Gibbs, Sam and Natasha both have agreed to stay and help you if you want their assistance." Maria stated, this confused Gibbs he had followed them out and so far none of them had said anything to each other. But he could see that both Natasha and Sam both wore serious expressions, he didn't know why but he was nodding his head in agreement but there was something in their eyes that had him thinking they knew something…something important. "Good, I will send an agent over with those reports." Maria added hopping in the elevator with Shaw, she gave Natasha a pointed look before the doors closed leaving the two agents surrounded by NCIS. Sam made the gesture for them to return to their desks which they did, she found it uncomfortable being the centre of attention but she looked at Ellie and saw the million and one questions in her eyes. Abbey came over to them with Jimmy two steps behind.

"Oh my god you look so much like Ellie." Abbey stated hugging Sam tightly to which Sam tensed under the contact and was proud of herself for not flipping the scientist.

"You must be Abbey, I heard all about you. Ellie has nothing but respect for you." Sam replied after Abbey stood back she was grinning now and Sam couldn't stop smiling back it was very contagious. "Formal introductions need to be made, Ellie this is Natasha Romanoff, Nat this is Ellie." Sam introduced they shook hands each one eyeing the other up.

"We have so much to talk about." Ellie stated looking at her sister,

"I am sure we do, but right now I think your bosses would prefer we get the case solved." Sam replied looking at Gibbs and Vance. Introductions were made by Ellie she pointed to each person.

"Gibbs you know, Director Vance, Tim McGee, Nick Torez, Jack Salon, Abbey and Jimmy Palmer." AS Ellie introduced her to Jack Sam couldn't help but state.

"Don't like shrinks. No offence."

"None taken." Jack stated but it being clear to Sam that she was assessing her.

Sam moved over to Ellie's computer much to the others surprise and logged on, this made Sam smirk she hadn't changed her password as she searched through everything they had on the case she could feel Natasha reading over her shoulder especially when she pulled up photos. One in particular it was of Clark's room.

"You know what is stumping me?" She asked Natasha but it was Jack that answered.

"What?"

"There should have been a photo of me next to his bed, we didn't take it, you didn't take it so who took it?"

"Could he have thrown it away when he realised you weren't actually dating him?" Nick asked

"My cover was still in tac, up until I escaped…besides he was dead by then."

"What makes you say that?" Gibbs asked they never told her the time of death and by the looks she hadn't yet read the autopsy report.

"You have my alibi on camera and yet you still think I did it. Hmm interesting." Sam stated looking at Gibbs before turning to the computer. "You seeing this?"

"Yeah, is that what I think it is?" Natasha asked leaning in closer to look at the screen.

"I need to see the body."

"What?" Gibbs asked

"The body. It still is here yes?"

"Yes."

"Right let's go," Sam said getting up

"Hold up what did you see?"

"You usually work at a fast pace yes?" Sam asked looking from Gibbs to Ellie everything she heard about this team told her they did.

'We are outsider, they still don't trust us.' Natasha stated over the link Sam turned to look at her.

'Then we will prove it.' Before she started walking to the elevator jimmy seemed to click that they wanted to go to autopsy so he jumped into action leading them down with Jack, Gibbs and Vance following. Gibbs instructed the others to stay up there and work. Palmer showed them the body but they didn't talk he found the silence unnerving. He had no idea what they were looking for. Natasha seemed to spot it first pointing it out to Sam who agreed. The others didn't see what they saw it was only bruising and nonlife threatening injury that occurred during his beating.

"I need Torez." Sam stated moving to the door but Gibbs blocked her for leaving.

"Start talking."

"I need to check something first, Torez is Clark's height and weight he will be perfect to check my theory."

"What is your theory?" Jack asked

"You might want to hope I am wrong." Sam stated moving around Gibbs heading out the door. Jack turned to Natasha but she seemed to shrug indicating Sam was the one to explain. Up in the ballpein Torez was very nervous as he stood there with both SHIELD agents circling him. Natasha nodded her head then indicated for her to go first.

"Agent Torez I want you to try to stop me."

"What?" he asked surprised as Sam touched his ribs then went to touch his shoulder but Torez blocked her, Sam moved around him trying to get to the point she needed. Stopping after her attempts failed.

"Not my height, if she was my height he would have different bruising. All yours. Again agent Torez try to stop Nat from touching you."

"What?" this time his voice cracked as he knew Natasha was an Avenger.

"Don't worry I am not going to hurt you. 10%?" this time she asked Sam

"Best to make it 8."

"8 what?" Torez asked nervously but his question went unanswered as Natasha started touching him with ease it being clear she wasn't even trying he stopped her twice. She stepped back shaking her head.

"I know ways to make those marks but no one my height will, we need someone in between." Natasha stated

"Or Taller." Sam said looking at Abbey then down to her boots. "Nice boots."

"Um Thanks?" Abbey asked she was standing next to Ellie Gibbs seemed click what she was wanting.

"No." he stated firmly

"She just needs to try to touch him here, here and here." Sam stated pointing to three points on Torez's body.

"What do you want me to do?" Abbey asked before Gibbs could answer.

"Try to hit him, here, here and here." Sam repeated pointing to three area's on Torez.

"What? No I am not touching Abbey." Torez commented seeming that he had slapped Sam's and Natasha's hands away he didn't feel comfortable hurting Abbey in any way. But by this time Abbey had moved over to him and touched him in the area Sam had pointed to after the second touch he tried moving away from her. Sam had her hand on her chin looking at what just happened. She looked to Natasha who wore a blank expressions she almost seemed bored but Sam knew she was alert. She gave Sam the slightest of nods barely recognisable in fact nobody picked it up except Sam.

"Right well that was a bust sorry for wasting your time, I need some air." Sam said moving to the elevator confusing everyone, when Ellie went to follow Natasha stopped her surprising everyone especially when she didn't follow her out. Something was bugging Gibbs and Jack little did they know they were thinking the same thing. Jack was the first one to click she moved over to Torez eyeing every spot they hit the first and third spot held no significance but the second there was a small mole on him. What did that mean? She turned to Natasha to find the red haired smirking at her before making her way out the ballpein following the way her soulmate had gone.

 **AN: What is it they discovered? Will Gibbs trust these agents for help? Where did Sam go? Tell me your thoughts, until next time.**


	8. Chapter 8

NCIS meets SHIELD c8

Finding her was easy and she was not alone. There was a woman standing in front of her and Natasha tensed when she saw there was a gun aimed at her soulmate, she stopped the NCIS agents from moving out. She saw their hands drop to their weapons or where they usually keep them but none of them were armed. Gibbs made Tim and Nick go back to grab their weapons he was concerned and confused seeming that Natasha seemed fine she was holding them back but making no attempt to aid Sam. Instead she was listening in to their conversation. Sam had managed to get her talking and she seemed angry it becoming clear on what happened.

"He still chose you, even when I enlightened him of your motives. What spell did you put him under that had him so loyal to you?"

"You were the one to tell them about me."

"They told me they would deal with you, clearly they did not do what I thought. Can't trust anyone these days."

"So you'd blow your cover to kill me?"

"He chose you."

"So you killed him?"

"I went to talk with him but then he got that photo of you and freaked out, he wouldn't listen…he made his choice now I must complete my mission."

"I doubt I am your mission. They wouldn't have given you access to NCIS if I was your mission…oh I see. Again you are going off book, you must have really fallen for him." Sam stated then she made her move one second she was standing there the next she had managed to disarm her but the fight didn't stop there.

To those watching it was hard to see what was happening, Gibbs really looked like he was about to step in as was Ellie especially seeming that the one Sam was fighting seemed to have produced a knife at some point but Sam was holding her own. She had the woman on the ground and they were wrestling for the knife that was when Ellie gasped breaking Sam's attention for a split second that was all it took. Torez and McGee turned up with guns drawn but by this point Natasha had stepped in and had knocked out the woman or so the NCIS agents hoped she was knocked out. Jack went over and felt for a pulse sighing she gave a small nod indicating she was still alive but that was when it became clear that Sam was hurt. Natasha was next to her covering her mostly from view she was muttering to her in Russian quietly what Gibbs picked up he could tell she was reminding her the importance of staying focused. Gibbs moved around her to get a better look at what happened and that was when he saw the blood stain on her upper abdomen. Natasha was applying pressure before tunring to Gibbs.

"Call an ambulance." She stated

"So not a scratch?" Sam asked but she sounded different, she sounded hurt.

"Not a scratch." Natasha laughed but the others could hear the pain in her voice, Sam was looking up at her. Tim was on the phone, Torez was securing the woman, Jack had come over and Ellie was in shock she seemed to jump out of it and knelt down next to Natasha.

"She's going to be alright yes?" Ellie asked, Natasha wanted to glare at her or shout but she remained silent focusing on her other half who still had not looked away.

"You're going to be fine, just stay awake…Nononono…Sam stay awake, keep those beautiful blue eyes on me."

"Tired." Sam mumbled

"Still need to stay awake. Help is coming."

"I should hurt right? Why don't I hurt?" Sam asked and this sent a wave of panic through everyone, this time she did look at Ellie. "Sorry, should have visited more, introduced Nat to you guys, you'll love her… wicked sense of humour should keep her away from Rob."

"None of that, you will have plenty of time to introduce her to us. Rob will love her." Ellie replied and that was when she saw fear in her sister's eyes. "You just need to hold on." Ellie added as medics rushed in and in no time at all she was in an ambulance Natasha was riding with her so the others drove behind her Nick and McGee stayed behind to secure the woman that stabbed Sam, Gibbs was fuming seeming she worked at NCIS he would get to the bottom of it but right now he was driving Ellie and Jack behind the ambulance heading for the hospital.

Ellie watched as Natasha paced the hallway waiting for the doctor to come out, Clint had turned up with Steve and were sitting across from Ellie watching her closely. Gibbs was next to her and she felt as though this was a dream and any minute now she would wake up but the dread in her chest was all too real and the noise of a busy hospital had her on edge. She felt as though she should say something to her but when she tried talking with Natasha she growled at her so she let her pace. She shot up out of her seat when Natasha stumbled in her pacing and grew concerned when Clint jumped up to brace her. She didn't think the Black Widow could stumble her eyes were glued to the door that would lead to Sam and before Clint could stop her she opened the door and ran down the corridor. She was surprised at how she could open the door then thought better of it seeming she was a spy.

Ellie went to follow but froze when a doctor came out not surprised at all to find Natasha running down the hall he didn't stop her, he was just glad that Clint was following her and as soon as Ellie saw his face she knew. Her sister would not be waking up and she wouldn't get the chance to argue with her over her job or gush over how she knew the Avengers.  
The Doctor started the whole I'm sorry we tried everything we could speech but her ears were ringing and she didn't really hear it. She looked down the hallway expecting Sam to come walking out, smiling at her as if it was a big joke but Sam did not come.

 **AN: So there you have it. What do you think? The story is not over yet. What happens next? Stay tuned. Until next time.**


	9. Chapter 9

NCIS meets SHIELD c8

 _Previously… The Doctor started the whole I'm sorry we tried everything we could speech but her ears were ringing and she didn't really hear it. She looked down the hallway expecting Sam to come walking out, smiling at her as if it was a big joke but Sam did not come.  
And now…_

"I need to see her." Ellie said

"Of course, be aware her soul mate is with her." The doctor replied before leading her down the hall she grabbed Gibbs before though she needed his support. She entered the morgue where Sam was on a table and Natasha was sitting next to her frozen looking at her soulmate. There was a doctor in the room but he was standing off to one side afraid of her and Clint was there too his face a mask as he tried to hide his feelings. Ellie didn't know what to do, but when he gaze landed on her younger sister she couldn't stop her feet from moving to the table. She has seen death before, in her line of work she is used to seeing a body on the table but seeing a family member was a whole new story. To her it looked as though Sam was asleep and could at any moment just sit up and make a sarcastic comment as to why they were all watching her. Still Natasha had not moved when Ellie went to touch her, to run her fingers over her cheek Natasha's hand shot up and grabbed it stopping her from touching her. Ellie actually yelped in surprise.

"Nat she's family." Clint stated he had moved next to his partner and had a hand on her shoulder he felt her slightly shaking so pulled her in for a hug, giving Ellie time with her sister. Natasha started thumping his chest as he held onto her. The door opened and Maria came in with two men in suites Gibbs looked them over.

"You knew she was in the building?" Gibbs asked Maria remembering the silent conversation she had with both her agents.

"I did."

"Why didn't you just arrest her?"

"Sam wanted you to hear the truth. She said she knew you wouldn't rest until you did and because of that she had to stay to prove it to you."

"She didn't have to prove anything to me."

"You mean a lot to her sister and her sister meant a lot to her so I allowed it…I thought…" she stopped and that was when he saw it a small crack in Commander Hill's armour she was blaming herself so he lessoned his glare.

"Who was she?" he asked

"A spy."

"Spy?" He asked confused as Maria went over to the bag of Sam's belongings and pulled out the recording device that Sam had used to catch her confession.

"She recorded her conversation." Maria replied handing it to Gibbs he noticed that Maria was still holding the bag of her belongings.

"Maria I want to interrogate her." Natasha stated

"Sorry Nat you can't."

"She's a spy who knows what else she knows. Why was she here?"

"I know you want answer but we need her alive, she is in NCIS custody." Maria stated and Gibbs was surprised that Maria held onto Natasha's glare because he knew if she glared at him like that he would look away and back down. "Coulson prepare the body." Maria instructed he nodded looking over the younger agent, he had recruited her and felt a responsibility for her, he was there when she met Natasha it seemed fitting he would return her home.

"What?" Gibbs asked

"What are you doing?" Ellie asked

"We are taking her home." Maria replied once again her expressions revealed nothing she was stone faced as Coulson led two other agents that looked like doctors into the room where they started prepping the body after getting Natasha's confirmation.

"You don't have to…" Ellie began

"We will accompany her home, I have sent an agent to deliver the news in person."

"My family thinks she is a piolet." Ellie stated to which Maria gave a tight smile.

"Her cover is still in place, she was murdered."

"SHIELD is a secret spy organisation they won't know who…" she stopped as Maria held up a badge that was an FBI badge.

"We have done this before." Maria replied, "Will you accompany us back?"

"Us?"

"We have a plane waiting, we will take care of everything." Maria replied but was now looking at Natasha that was when it became clear that she wanted Natasha out of the state and away from her killer. She looked at Gibbs who gave her a small nod, he will go down later but first he had some business at the navy yard to take care of. He will send Jack with her then once everything is wrapped up he will bring the others to her.

 **AN: another short chapter just to give context. Until next time**


	10. Chapter 10

NCIS meets SHIELD c10

Everything after that seemed to be a blur of movement one minute they were at the hospital next they were on a plane and Ellie was looking at a wooden box in the middle of a plane. Things started moving again when she was home everyone was there and they were a wreck. Her mum was in tears, her father was silent it being clear he had been crying her brothers Rob, George and John each one red faced in anger or tears she couldn't tell she was numb. George was angry at himself for not checking on her sooner he felt it was his responsibility as the oldest to look after his younger siblings and it was hitting him hard that he failed his youngest.

Her mother was all over Natasha making sure she was alright but it seemed she was a ghost in a shell Clint was there as was Maria both of them keeping a very close eye on her to see if she would lash out. Coulson and May also were there told they were co-workers. Her family home that she grew up in was leaving a sour taste in Ellie's mouth as everywhere she looked reminded her of Sam and the house itself felt very small especially when the Avengers turned up surprising her family and friends that turned up to offer condolences. Hours turned to days and Ellie lost all track of time, Gibbs and the others turned up she was grateful of Abbey's hugs. Jack was a huge help she stayed the whole time. Ellie burst into tears when John had made the same comment that Sam had made about Abbey's shoes, and how George didn't like shrinks when he discovered that Jack was a shrink. Natasha observed the Bishop family mostly in silence trying to picture what it was like for Sam when she grew up, at night Ellie would come and sit with her on the porch, Clint was always not too far away the silent observer with a hawks eyes. The slightest change in Natasha's attitude he would be next to her in a flash, this had Ellie wondering how well he must know her to get reactions from her.

On the third day Natasha had a fight with Clint in the backyard, it was physical and Ellie's family wondered if they should intervene but Clint knew this is what Natasha needed, he let her kick the living daylight out of him and then she cries and he held onto her tightly. Natasha apologised for her behaviour but none of the Bishop's held it to her they accepted her right away since Ellie turned up with her stating she was Sam's soul mate.

The next day was the funeral and Ellie was in tears most of the time so she couldn't see through her tears for most of it, she did see several agent in the small church and at the graveyard she saw so many people in suites it was nice to know she had friends. She met some of them a blur of names, she was surprised that Natasha stayed near the back of the church or off to one side, she didn't do a speech which the others couldn't blame her for. Nice things, so many nice things were told about her sister. Gibbs and the others were in the crowd they were there for her and had offered their own condolences to the family. Tony Stark and the other avengers were there trying to be low key but even at a funeral it was hard. Ellie had to admit they cleaned up nicely and appreciated that they tried not to draw too much attention. Her parents had an incredible speech and George spoke on behalf of his siblings they nominated him as Ellie knew she would be a mess and wouldn't be able to form a decent sentence let alone a speech.

Before she knew it Ellie was looking at a piece of concrete with words on it, where her sister was put to rest. As the crowd disappeared returning to the house for refreshments Ellie noted that now Natasha had moved over to the grave stone and plonked herself down next to it bringing her knees up to her chin she simply sat there. Ellie looked around to see at least four different people in suites waiting for her and felt herself dragged away by Rob. This part she hated so many condolences from people that hardly knew her that is what set Ellie's teeth grinding, especially when Sam's childhood bully turned up Ellie couldn't face him so she returned to her room to find sanctuary. But was stuck looking at Sam's door, and memories of her childhood came flooding back. She found herself crying once again. Most of the people were finally gone leaving family and very close friend behind. Ellie went in search of her brothers finding them in the attic or their secret fort, drinking the scotch from the chest the four of them sat in silence each one reflecting on their own memories of Sam.

"You remember when she was ten she locked herself up her, none of us knew what she was doing and none of us could entice her to come down."

"She had an argument with dad so was advoiding mum. She made a gift for him as an apology, she fixed one of his tools that you had broken Rob." Ellie replied.

"I didn't break it George did." Rob rebutted

"Sam took the blame for it." George added, "I never thanked her."

"She knew you wanted to go out on Friday with Susan and if Dad found out he would have grounded you for certain. She told me that night…she was grounded for a week because of that."

"She got me back for blaming me on the fence incident." George stated

"What did happen with the fence?" John asked

"I don't know what she did all I know is I got the blame and lost two Saturday's because of it. And I had to help repair it. I got like three splinters." George stated seriously before they all started laughing.

"She was always doing something crazy…"

"I always thought she would be the one of us that would do something important with their life." Rob stated looking down at his glass, once again turning the mood sour.

"To Sam." George raised his glass

"To Sam." The others echoed Ellie felt that wave of guilt gnaw at her stomach, she was lying to her family. Her sister did do something important with her life, she was making a difference. She was a hero and she couldn't tell them, she couldn't tell them that she fought an assassin and was helping with her case. She couldn't tell them that she was a spy, "why did she have to die, she had so many questions."

"What was that El?" Rob asked

"Huh?"

"You were muttering something."

"Was I? Sorry today has been a long and emotional day."

"Do we know how long Natasha will be staying?" John asked

"She's still at the cemetery." Ellie stated

"What?"

"Don't worry Hawkeye was with her and other agents." Ellie hiccupped

"Agents?" George asked

"What?" Ellie asked

"What agents El, you said she was with Hawkeye and other agents."

"Well I guess they are there with her to make sure she doesn't do something harmful." Ellie stated now sobering up she looked around her brothers to see if they had brought it, one second past then another before the three of them shrugged, none of them saw Ellie sigh with relief before she left her brothers to go downstairs to spend some time with her mother.

1 week had passed and Ellie was still at home with her family it felt as though the world was moving on, every now and then a condolence would be made but strangers stopped coming around and most of their friends had left to return to work. Gibbs had told her to take her time and would see her when she was ready to return to work. She found herself busy helping out around the house but soon there was nothing else to do and that had her stumped, the more she did nothing the more she thought about Sam. She was having nightmares of seeing Sam dying over and over, getting stabbed for her all so she could close a case she got her confession but at the ultimate cost.

Natasha had left the day before finding it too hard to be around Sam's family the others understood Natasha was from the life that Sam did not talk about, was from a different family that she had made away from home. Natasha did leave a contact number that if they needed anything she would be there for them. Her mother had supplied her with enough food that could last her a week, Natasha bowed her head in gratitude planning to leave it with that but that was not the Bishop way she was hugged by them all. Rob even managed to a get a photo with her to add to his collection of a photo with all the avengers when they visited. Stark had paid for everything leaving a number that if they needed anything they just had to call, he made it clear that what he thought about Samantha Bishop to which they were grateful for.

 **AN: I had blurry eyes as I wrote this thinking of Ellie and her family…tell me what you think. Until next time.**


	11. Chapter 11

NCIS meets SHIELD c11

Getting back to DC was hard when she finally left her family behind and walking into work was one of the hardest things she had to do, stopping in the spot that her sister was hurt in sent her heart racing she didn't hear the person behind her talking to her so when he placed a hand on her shoulder she jumped only to relax when she saw it was Gibbs.

"You alright?" he asked knowing she might hate that question but his concern for her was genuine.

"Yeah…I mean I didn't think…this is where is happened. And I was standing right over there and couldn't do anything to stop it." Ellie replied before walking to the elevator where they rode in silence up to the ballpein.

"You good to come back to work?" he asked

"I ran out of things to do there and everyone was getting edgy. Everything reminds me of her and it all feels surreal. I need to work." Ellie finished finally answering his question to which he gave her a nod, when the others saw her she was once again asked that question this time she was also hugged.

…

2 months had passed and things had settled back down to a normal routine, Ellie was there for Sam's killer's trial and she was persecuted for espionage and two degrees of murder. Work was back to normal solving cases, she was at her desk writing a report when Nick came running in and changing the channel on the tv.

"Ellie you have to see this." He stated switching it to the news where footage of an attack was taking place and the avengers were there fighting away.

"Where is this?" Ellie asked getting taking her phone to do research, to get information.

"France." Nick replied as footage of Captain America fighting off the weird looking creatures before going to save some civilians. He picked up a child and carried him to safety.

"Another alien invasion."

"This isn't a full out invasion though according to the news it's a small group of Aliens that started killing people." Nick replied

"Hey have you guys seen the news…oh you are seeing it now."

"What do you think McGee?"

"I hope it's not another alien invasion."

"They say it's not."

"Yes but news can be misleading…there is things such as cover-ups." Tim replied placing his bag next to his desk.

"She seems good." Ellie stated finding any footage of the Black Widow.

"Have you heard from her at all?"

"Not her, but that Phil guy. I think he was checking up on me for her."

"She was at her sentencing…I thought she was going to kill her for sure."

"Clint, Maria and Steve were with her. But it also seemed they wanted her dead too." Ellie replied but McGee and Torez knew this was getting to dangerous waters.

"So that theft report, you finished it?" Tim asked changing tactic."

"Yes, all finished and sent off."

"Good, have I shown you the new baby pictures?"

"I haven't seen any recent ones." Ellie replied so that was how they ended up talking about babies until Gibbs turned up with a case.

Another month passed and Ellie was in the streets of DC walking to one of her favourite café places when she froze, standing across the road from her was Sam, with shorter darker hair but it was her she went to call out to her but a truck passed by forcing her to step back once it was out of her way she looked over the street but Sam was gone. Was it really Sam? Ellie asked herself scanning the people walking either way but could not see her she ran back to her car and drove to the Navy Yard running into Abbey's lab happy to see Tim there already she asked her friends for help. They were so focused on the screens in front of them they didn't see Nick enter the room, he stood there for five minutes trying to decipher what they were doing finally he gave up.

"Guys what are you doing?"

"Nick when did you get here?" Abbey asked

"Five minutes ago, what are you trying to find? Oh I know this street, there is a great café there."

"We are searching the cameras in the area." Ellie stated carefully.

"I can see that but why?"

"I thought I saw someone…"

"Who?"

"Sam."

"But she died…you saw her body." Nick replied gently

"I know, but I swear Nick I saw her…or I think I saw her." Ellie stated looking down, they had been searching all the cameras and so far nothing. Did she really see her or was it because she wanted to see her so she just imagined it. "It looked exactly like her…I'm sorry guys I didn't mean to waste your time."

"Hey none of that Ellie, we are here for you. If you say you saw her I believe you."

"Thanks Abbey but now I think it was just a case of mistaken identity." Ellie said leaving the lab completely missing the glances the others were sharing with each other.

"I thought she was doing well?" Nick asked making sure Ellie was actually gone.

"She has been, maybe it was someone that looked like her and it got her hopes up."

"But Sam is dead, I mean we all saw the body."

"Did we? Sure we saw it at the hospital but then those SHIELD agents took her. They could have given her a drug to make her look like she was dead and then whisked her away." Tim stated.

"Ellie stayed with them, I think she would have seen that." Nick retorted

"Oh right. Never mind." Time mumbled

"Still I think we should keep a close eye on her today." Nick stated, but he was looking back at Abbey who had returned her attention back to the computer. "Abbey do you agree?" he asked

"What? Oh yes, keep an eye on Ellie of course. You better head back up to the ballpein Gibbs will be wondering where you are." Abbey replied and after Nick and Tim looked at her confused they agreed to leave.

"Do you know what she was doing?" Nick as Tim as they left her lab heading for the elevator.


	12. Chapter 12

NCIS meets SHIELD c12

As Nick and Tim entered the ballpein they found Ellie at her desk just looking at her computer screen unaware to their entrance, they both once again shared a concerned expression with each other before sitting at their own desks and not a minute later Gibbs came in and called them out they had a new case. Nick kept sending Ellie concerned looks and it was starting to get to her but before she could say anything about it they had arrived at the crime scene. So instead she got out of the car and headed over to Gibbs, he directed Nick on witnesses and coordinate with the local police that were there with McGee and Ellie was on documenting the evidence so she pulled out her camera and started taking photos. Jimmy pulled up and started his examination so Gibbs stood there waiting for him, Tim came over to run fingerprints to find that it did match the name on her uniform the victim was Lieutenant Kelly Charles. So he sent Nick and Tim to go to Norfolk where she was stationed now that the scene was documented and Jimmy was ready to move her back to the Navy Yard. Gibbs took Ellie back to do some research on her. As Ellie pulled up her record which to her seemed perfect, she had worked hard and rose through the ranks she had several recommendations, she had done two tours over in Afghanistan and was a recipient for a purple heart. She knew that Gibbs would want more so she dug deeper and into Kelly's life. When Tim and Nick returned she felt as though she knew Kelly Charles, Gibbs then sent Ellie and Nick to her apartment to search it. While Gibbs was taking Jack to go and talk with her family that lived just outside of the city. McGee would be running things from here by checking up with Jimmy and Abbey then he would help Abbey with her laptop, when Ellie and Nick brings it back from her place.

Ellie was once again driving to the apartment, this brought up the topic that Nick always brings up seeming that he never gets to drive. This made Ellie smile as the banter once again started and didn't finish until she had arrived at their destination. They searched her apartment taking her laptop and documenting it only to get interrupted by a roommate who returned as they were searching the place. Nick managed to calm her down and got her statement as Ellie continued to search the place but nothing really was out of the ordinary. As they were leaving her roommate made them pause as she asked if her death had anything to do with the Marine she was helping. They got the full report from her which wasn't much considering but it was enough.

"Apparently Kelly was helping out a fellow Marine named Teddy, that was all her roommate remembered. That Kelly was worried about Teddy and scared that he was going to do something reckless." Ellie stated over the phone back in the car.

"Right I will search the names of those in her unit to see if any of them are named Teddy." McGee stated

"I already did, there was one that used to be in her unit his name was Theodore something…"

"Theodore Williams." McGee replied looking over Ellie's research. "He was medically discharged."

"Yeah her last tour, she was made the recipient for the purple hear because she dragged her comrades away from the Humvee while under heavy fire, getting them to safety, it was the only reason as to why Theodore and another made it back alive." Ellie stated

"You remembered that from her file?" Nick asked

"You know I have a good memory. Plus it was inspirational." Ellie shrugged.

"Right you two should head back to Norfolk see what you can find out about Theodore while I try and find him." Tim replied

"We can do that." Ellie stated at the same time as Nick's

"Who put you in charge?"

"Gibbs." Both McGee and Bishop replied to Nick together. He didn't reply on ended up grumbling something under his breath that neither one heard. Ellie drove back to Norfolk where they talked to Kelly's CO he was surprised that they were back seeming that he had already answered Nick and Tim's questions earlier. He became even more surprised when they asked him about Theodore Williams.

"Evidently he was a good Marine, he lost one of his legs in Afghanistan and barely made it back alive. Kelly stayed with him even when he pushed everyone away, she stayed to make sure he was going to be ok. That was the kind of Marine Kelly was, always concerned about her fellow brothers and sisters in arms. She cared for him even after a trashed her car, he blamed her for bringing him back alive broken."

"Would he hurt her?" Nick asked

"No, not now at least last I heard he worked things out with her, this was 9 months ago."

"What about the other one? The 2nd Marine that came back injured was he discharged too?"

"No, he has returned to active duty. He passed his psych and physical…he was grateful for Kelly too, she helped him also by training with him."

"Sargent when was the last time you heard from Kelly?"

"Yesterday, she came in even though it was her day off, I already told you this." He said looking to Nick.

"What was she doing?"

"She came in and looked over some files."

"Do you know what files?" Ellie asked this grabbed Nick's attention he didn't say this before.

"You didn't say this before." Nick spoke up.

"When you left I thought over everything that happened yesterday…And it would be logged to see what files she brought up." He said answering Ellie's question he turned to his computer and brought up a list of reports that Kelly looked over. "This is strange, she has brought up personal files but none of these names are in her unit, two of them have been discharged.

"Can we have a list of those names?" Ellie asked he nodded then printed them off for the two NCIS agents. Nick and Ellie then returned to the Navy Yard to report back to Gibbs.

 **AN: Well back to business or is it? Until next time.**


	13. Chapter 13

NCIS meets SHIELD c13

Everyone was back in the ballpein working away at their desks trying to find a link between Kelly and the list of names she was researching. McGee was down in Abbey's lab working away on the Lieutenant's laptop while Abbey worked on the evidence she was given from the crime scene. Nick was working on trying to locate Theodore now that Tim was working with Abbey leaving the other names on the list for Ellie and Gibbs with Jack's help she had offered to work this case.

"Found something." McGee came running into the ballpein grabbing his gear.

"McGee what did you find?"

"Not me Lieutenant Charles on her laptop she kept coming back to this address I figured we go and check it out."

"Right, grab your gear." Gibbs instructed making it clear they were all going. They took two cars to the address that Tim had forwarded them that led them to a warehouse.

"Do we need a warrant?" Nick asked

"No this is foreclosed, condemned to come down. I called the bank and they said we could enter." Tim replied. Ellie looked around the outside of the warehouse and it certainly gave off a bad vibe so she wasn't surprised that Gibbs made them suite up and enter the warehouse with weapons drawn.

"Abandoned warehouses give me the jeebees." Nick stated but he as the others were focused on what they were doing.

"Not abandoned." Gibbs replied as they then all heard it hushed voices whispering down in the office area the lights were on. So the NCIS agents moved in taking caution, it was a good thing they were as that was when the gunfire started. They all dropped for cover as bullets hit the area around them. Ellie was with Nick and Jack leaving McGee with Gibbs across from them, Ellie looked over and saw McGee calling it in as Gibbs was keeping him covered. Torez was firing back joining Gibbs so Ellie did likewise. She tapped him on the back forcing him to look at her.

"Cover me." She shouted

"What?" he asked but she didn't have time to repeat it as she started moving she heard Torez swear but nevertheless he covered her as she sprinted to the next pillar in time as she heard bullets make contact with the concrete. She turned back to them but they were also covering behind their own pillars. Right now Ellie was the one in the lead so she gave cover and waited trying to hit someone she jumped when she felt a hand on her shoulder to see Jack standing behind her.

"That was crazy." Jack told her

"I know, no doubt I will get an earful later but look." Ellie pointed out that those firing on them were taking cover behind some large crates. "We couldn't see that before." Ellie stated

"Right what do you want to do?"

"Cover the others, let them move up."

"My ammo is sparse." Jack replied making Ellie think on hers, she too was getting low.

"Then we need to resolve this before we run out." Ellie replied about to start shooting again but an instinct told her to wait, it was a good thing she did as bullets ripped into the pillar they were behind forcing both of them to crouch down that was when the lights went out.

"That can't be good. New plan?"

"They seemed to be focused on us."

"I don't think that is a good thing." Jack replied as more bullets could be heard, that was when something caught in Ellie's peripheral vision forcing her to look up. A shadow? She looked up making sure no threat was coming from above. That was when it moved again but it wasn't going for them or anyone from her team. More gunfire was heard followed by thumping as bodies dropped. She was trying to see through the darkness but it wasn't really happening.

"Did you see that?" Ellie asked

"What?"

"I think someone is up running along the walkway up there." Ellie stated still looking up trying to decipher the shadows.

"I can't see anyone?" Jack stated as more gunfire was heard

"Is it just me or is there less guns firing?" Ellie asked

"You're right." Jack stated after thinking about it and concentrating on the gunshots. There was more yelling and someone screamed then the gunshots stopped. "Could be a trap?" Jack stated but Gibbs took this chance to move up with Tim and Nick.

"You're crazy." Nick told Ellie when he got next to her Gibbs made the signal for silence then the NCIS agents moved forward and were very surprised to see what was behind the crates. Tim lowered his gun looking over the dead bodies each one shot, a couple of them were still alive moaning away and their weapons were discarded.

"What just happened?" Nick asked

"That is Mike Gileon. One of the Marines Kelly was investigating. He was dishonourably discharged." McGee stated not answering Nick's question mainly because he didn't know.

"Looks like we had a guardian angel." Jack replied looking over the bodies and how some of them had fallen, "it did seem someone was on the walkway." Jack added looking to Ellie

"What?" Gibbs asked turning to Ellie

"I thought I saw a shadow up there, maybe I didn't. I don't know what I saw." Ellie replied checking her own weapon. "Good thing I was on my last mag." She added

"I only had three more bullets left." Nick stated the others weren't any better. That was when Gibbs realised how bad off they were if it wasn't for whomever saved them he didn't want to think about what would have happened. Speaking of he looked at Ellie and gave her a glare at her recklessness. As Jack secured those still alive and Tim and Torez went to clear the rest of the building.

"Gibbs I know that was reckless and I didn't think it through but I am fine. I was trying to protect you guys, I knew we had to move forward or who knows what would have happened I was the one to spot where the shooters were hiding." Ellie tried to explain but his glare remained and she actually shuffled on her feet looking down. "I would apologise but I know how you feel on that…"

"Gibbs you may want to see this." Torez called out saving Ellie from his glare, she did know that it was not over he will talk with her later about it. Gibbs went into the office area where there was another two bodies but what really grabbed his attention was the stockpile of weapons on the table and the bags of cash.


	14. Chapter 14

NCIS meets SHIELD c14

"What exactly did we stumble on?" Tim asked

"Weapons smuggling? Weapons deal? Whatever it is it is dodgy and most likely got Kelly Charles killed." Nick replied

"Alright document everything." Gibbs replied and they all got to work, ambulances and police turned up but they gave authority to Gibbs and did what he wanted. He and Jack had searched the perimeter trying to locate who could have saved them but there no sign of them. Vance turned up when Jimmy did and well he was not impressed with the mess. When the FBI turned up a power grab started it was finally turned into a joint investigation which Gibbs was not happy about. Especially when the order was given the lead agent practically told him to go catch his killed and leave this to them. Jack found it interesting to see the vein in Gibb's forehead seemed to pulse as he held his anger in. He ordered McGee and Torez to stay here while he took Ellie and Jack back to the Navy Yard. NCIS was given some leeway seeming that Palmer turned up first and started examining the dead bodies. Gibbs just knew his case got a whole lot bigger and they will be working until it got solved. Back at the Navy Yard Gibbs and Ellie worked on in silence and when Nick and Tim came back they felt the tension in the room, Jack was standing off to one side watching them so Nick and Tim made their way to her.

"How long has that been going on?"

"They went in the elevator, it stopped and when it started again they came out and have been like that since." Jack replied knowing of Gibb's impromptu meetings in the elevator but this is the first time she had witnessed it not to have worked and possibly made the matters worse.

"Have you tried talking to them?" Nick asked

"I did and got glared at by both of them…it gave me chills." Jack stated

"So you decided to hide over here and spy on them?" Tim asked this made Jack look at him.

"What I am not spying on them…"

"Are any of you going to get some work done or are you going to stand here talking?" Gibbs asked from behind them making them jump and turn to face him, Tim and Nick jumped to attention and headed to their desks while Jack only continued to stare at him. "What?" he asked but Jack only shook her head before walking off. Gibbs sighed before returning his attention to his two agents that had returned.

"Boss about before…"

"Drop it, what did you find?"

"Nothing…" McGee paused at the glare he was getting from his boss. "I mean we found their books but it is all in code so will take some time to decode it. The FBI took the fingerprints and the injured men." McGee informed him and when Gibbs shifted his weight to one leg McGee tried to come up with something that would please him.

"None of those men in the warehouse was Theodore Williams so we were going to head over to his last known address." Nick stated coming to McGee's defence.

"Go." Gibbs said deciding to head down to Jimmy to get an update. Ellie remained at her desk, knowing that Gibbs would be keeping her on desk duty for the remainder of the case, or that was what he told her in the elevator.

Gibbs entered the autopsy room to see Palmer looking over one of the dead guys from the warehouse the one McGee recognised.

"What have you got Palmer?"

"Gibbs your early, I just got him back from the warehouse other than COD, gunshot to the head, I haven't anything else on him."

"What about our Lieutenant?" Gibbs asked

"Oh right. Lieutenant Kelly Charles, she was stabbed to the abdomen and bled out, she was stabbed 5 times but the first one would have caused the most damage."

"Was it long?"

"No, it perforated an artery. She would have died in seconds, she wouldn't have felt it."

"Do we know what knife?"

"That is up to Abbey to decide, along with the strange substance I found around the wound." Jimmy stated. "An interesting fact…and your gone." Jimmy said looking up to see the doors closing so Jimmy returned his attention to Mike Gileon. Gibbs made his way to Abbey's lab who was waiting for him when she heard the elevator ding, she pulled him into her lab and started talking so fast he had to make her stop and repeat and less since words.

"Sweat."

"What about it?"

"That is what was around her wound, the substance that Jimmy set up. It was sweat, I have it running through codis now."

"Do you know what type of knife?" Gibbs asked

"From the impression you would think just your standard combat knife, but it is not. See here the groove from the hilt. It was an M-9 Bayonet and guess who has this style of knife registered as their combat knife?"

"Who?" Gibbs asked and Abbey pulled up a photo making Gibbs smile he kissed her on the check before leaving the lab grabbing Ellie and Jack on the way out and heading for Norfolk.

 **AN: who did it? I know this chapter was short, for dramatic effect what do you think? Until next time.**


	15. Chapter 15

NCIS meets SHIELD c15

Gibbs led both Ellie and Jack through the halls, most personal looked on with interest it being clear they were agents and were on a mission. Everyone got out of their way as they walked to the Officer's lounge.

"Agent Bishop what are you doing back here? Did you find out who killed Kelly?" Sargent Michael asked.

"Is Lieutenant Cullum here?" Gibbs asked and Michael could tell he was the one in charge.

"Cullum?"

"He was the one that led us to you last time we were here."

"I know who he is and yes he should be at his desk. Why?"

"Which one is his desk?" Gibbs asked to which Sargent pointed out Cullum's desk but was surprised to find it empty.

"Jenny where did Cullum go?" Michael asked a female officer who was at a desk across from Cullum's

"He was here just a second ago but when word spread the NCIS was back he got up and left, he went towards the bathroom." She replied Gibbs entered the bathroom while Ellie and Jack waited outside but ready to enter if Gibbs needed it. Jack was holding the door open and Ellie scanned the crowds of people who were all growing interested at what was happening.

"Lieutenant Cullum." Ellie shouted recognising the man who had just slipped out of the door. "Jack, Gibbs." She shouted giving chase she heard Jack following her and knew Gibbs wouldn't be too far behind. She rounded the corner in time to see Nick tackle Cullum to the ground before cuffing him while reading him his rights, the whole time Cullum was swearing away.

"What are you doing here?" Jack asked

"Abbey called, the dna on Kelly matched Cullum's." Tim replied as Nick pulled Cullum up and started walking him to the car. As they were walking out Ellie had to double take she faltered in her steps but thinking she saw Sam again, but when she turned back to the woman that was walking in the different direction she realised it wasn't her. Her shoulder slumped in defeat she got back in the car and drove with Jack back to the Navy Yard. She was surprised it was her and not Nick but Jack had said he wanted to be in the car with Gibbs and Cullum as McGee drove them back. Ellie saw right through it, she knew that Jack was here to check up on her so she focused on driving.

"How are you doing?" Jack finally asked, she noticed how Ellie seemed to clench the steering wheel ever so tighter.

"I'm fine."

"You think you saw your sister…on the street and in the warehouse."

"What?" Ellie asked turning to look at her, she didn't tell anyone that she thought it was Sam that saved them in the warehouse.

"Eyes on the road." Jack shouted as Ellie turned back to the road hitting the break so she wouldn't tailgate another car.

"You kept looking up with hope in your eyes, I was right next to you. That and when Gibbs asked about it you second guessed yourself unsure on what you saw."

"Ellie Sam is dead."

"I know damn it, I know. I saw her body, I held her in my arms, but still."

"You want her to be alive."

"Wouldn't you? I don't know I was thinking if I worked for a secret spy organisation and my identity was revealed and my family was put in danger maybe…"

"Maybe they faked her death?"

"Gibbs saw her fight, it seemed like she should have handled herself…"

"You blame yourself." Jack realised

"I distracted her, it was my fault." Ellie replied through gritted teeth and clenching the steering wheel tighter.

"Ellie…"

"Can we not have this talk, you're going to tell me it's not my fault, I will act as though what you say is true even though you know I will lie. Please Jack, I am dealing with it, let me deal with it my way." Ellie said.

Back at the Navy Yard Gibbs interrogated Cullum it took all of five minutes for him to confess, he was part of the arm dealing taking weapons that were being sent back from Afghanistan and how some would disappear over time they got a decent amount they got together to sell them, his job was to cover up the paperwork of the missing weapon how everyone thought they were disposed of. He gave up names of the others that he knew. And how he regretted killing Kelly how he really liked Kelly but she was digging into their whole operation and he had to deal with it or the others would have dealt with him. Over all Gibbs was happy with the outcome.

"You know what I don't get?" Nick asked

"What?" Tim asked

"What happened to Theodore Williams?" Nick asked

"He just made contact with us, apparently he listened to Kelly he refused their offer and had spent the last week laying low in a family's cabin." Jack stated entering the observation room with Vance. "He was devastated to hear about her death. Sargent Michael is with him now, he will make sure he is okay, for Kelly."

"So is that it? Case closed?"

"I believe so, well done all of you great work. Go home get some rest." Vance stated to which the others nodded knowing they would have to write up their reports before they could go home but it shouldn't take that long. McGee was the first to leave, followed by Torez leaving Gibbs and Bishop as she finished she looked at him. She knew Gibbs had kept sending her glances so no doubt Jack had spoken to him, then again he never seems to miss much.

"Goodnight Gibbs." Ellie said leaving the Navy Yard returning to her apartment she kept replaying Jack's conversation in her head. She will do it her way so grabbing her bat she headed to the cages.

She had been there for an hour when she felt eyes on her, looking around to find no one there she continued hitting, or in this case missing the ball. As a memory surfaced.

'Call that hitting? If you're going to play at least hit a ball.'

'Go away Sam.'

'Come on El, what happened to the great Elinor Bishop who dreamed of being a pro baseball player?'

'She grew up.'

'Come on Grandma could hit the ball.'

'Could you?'

'That is why I am standing out here and you are in there missing the ball…I don't see the point of this sport.'

'It calms me.'

'It calms me.' Sam parroted before cracking up laughing and Ellie could swear she could still hear laughter in the air. She had tears once again in her eyes, she could just picture her sister standing behind her shaking her head, and what she would say. 'How are you going to hit the ball if you can't see?' She focused on the ball coming and whacked it, the sound of a ball hitting a bat echoed around the quiet deserted bat cage. "You would have liked that one."

'Look at that ladies and gentlemen she can hit the ball. Homerun oh my goodness.' This made her turn around and she could just picture her standing there with a big smile.

"You know if you are going to haunt me you could do it to me when I am alone."

'You are alone.'

"I think I am losing my mind." Ellie said turning back and hitting the ball once again but this time no voices were heard she missed three more before hitting the next.

"That was a good one." A voice made her jump and turn around only to relax when she saw it was Gibbs.

"Gibbs you startled me."

"You okay?" he asked noting her tears, she quickly brushed them away. Before stopping the balls and coming out of the cage, she put her bat down and grabbed her water bottle. "Do you want to talk?" he asked, even though he didn't want to make her uncomfortable.

"How long have you been here?" she asked

"Not long…Who were you talking to?" he asked

"No one," she replied at this he raised an eyebrow at. "Sam, I remembered something and I could just picture what she would say." At this Gibbs only nodded remaining quiet giving her a chance to think.

"You will get through this Ellie, you won't forget but one day you will wake up and it will be easier." He stated grabbing her hand

"I take it Jack spoke with you."

"She did say I should speak with you." Gibbs replied "It has been a long couple of days you should get some rest." Gibbs said leaving her after she agreed she'd get some rest.

Instead of heading home though she went to a bar and spent the night out. She got lost in the music when she figured she had enough she left to go and call an uber. She didn't think she had that much to drink but she found herself stumbling down the street. She felt a hand grab her by the arm pulling her closer to them she turned to be facing a guy she had danced with in that club.

"Can I help you?" Ellie asked she could feel herself sobering up as her heartrate picked up.

"Hey doll I could think of one thing you could help me with." And he started pulling her along the street. She looked around hoping to see someone that might be able to help, but no one was out. He was pulling her passed one of the alleys when he let her go seeming he was yanked into the alley. She heard a scuffle and a small part of her brain was telling her to run, the other part, which was more sober now took over and she stepped into the alley to see the guy on the ground unconscious and someone she was not expecting to be standing there. Ellie took a step towards them but fumbled and ended up falling the person grabbed her and the last thing she saw was her sisters blue eyes before she passed out.

 **AN: What just happened? Was that Sam or was it someone else that Ellie wished it was Sam? Tell me your thoughts, until next time.**


	16. Chapter 16

NCIS meets SHIELD c16

Ellie woke with a groan, memories of last night seemed very fuzzy. The brightness of the room made her wince…wait her room? How did she get here? Sitting up she looked around yep it was definitely her room but she had a drip in her arm fluids she figured but who gave it to her, she could hear voices outside her door.

"We did not put you in deep cover so you could blow it." A voice stated angrily.

"He drugged her you couldn't possibly expect me to sit by and let him hurt her."

"No of course not, what about the warehouse?"

"We were on that before they turned up, I got Izzy out and so what saved them, they were not prepared."

"I know you want to protect her, but you can't keep breaking protocol to do it."

"Protocol? Coming from you."

"Fine she is home safely you need to go, I will keep an eye on her. Or you will have to deal with Maria and actually get transferred to Coulson."

"Fine just lecture her about safe drinking." Ellie had heard enough, standing up heading for the door only to grab the wall as a wave of nausea hit her, the door opened and Natasha entered carrying a glass of water and some painkillers.

"You are up. Here." She said handing her the glass of water. Checking the iv before examining Ellie over. "How do you feel?"

"My head is pounding, and everything seems bright. Natasha what are you doing here?"

"Keeping you out of trouble."

"So it was you in the warehouse?" Ellie asked to which she received a blank stare

"If you know what it good for you, you won't go around expressing those thoughts." Natasha replied and in that tone Ellie could read something lying beneath it, if her head wasn't pounding she would be able to think about it more easily.

"Were you talking with someone?" Ellie finally asked now that Natasha seemed happy with her health check she took out the iv. She once again received that hard look so she looked down deciding to change the topic. "I saw you in France." To which she received a raised eyebrow at. "Sorry it's just been a while since I saw you."

"You need to be more careful Sam wouldn't want you doing reckless things, what were you doing at the club?"

"Blowing off steam, we had finished a case and I was missing Sam." Ellie stated and watched as Natasha's gaze softened lightly.

"I miss her too." Natasha replied and they then moved out to the kitchen where Natasha made Ellie something to eat. As she was sitting down and eating there was banging on the door, she was surprised that Natasha went to go and open it. Nick was standing at the door and actually yelped when he saw who it was that answered it. He followed her inside to see Ellie sitting at the table and eating breakfast.

"Damn it Bishop don't you check you phone, you have had us worried." Nick stated when he saw her.

"We have the day off." Ellie stated confused

"And if you checked your phone you would see we were called in." Nick rebutted grabbing a piece of her bacon.

"I'm busy. Yesterday was a long day."

"She has slept most of the day." Natasha informed him and it was true it was after two.

"Nick I will meet you at work."

"I can bring you." he stated

"Goodbye Nick."

"Fine, but you better come or it will be Gibbs coming to see you." he said leaving as Bishop finished eating.

"You could call in sick." Natasha suggested

"That would only make them more concerned. No I will be fine. Are you staying around DC?"

"For a couple of days." Natasha replied as Ellie then went in for a quick shower when she got out she was expecting Natasha to be gone but she was there finishing putting the dishes away.

"I need you to do something for me."

"Oh?" Natasha stated looking up at Ellie

"Tell my sister that I am not mad, that I understand and that I can keep her secret just tell her to stay safe because if she dies I will give her hell." Ellie stated she had accepted why Sam would fake her death, to protect her and her family. She just wanted her to know that she knew and was not mad. "Tell her that I miss her and if she ever wanted to talk, I am here. Also thank her for last night and the save before that." Ellie said grabbing her bag and weapon before walking out the door knowing that Natasha would lock up, as she walked to her truck she felt like a burden had been lifted off her shoulders and that she could finally breathe again. She drove away from her apartment and headed to the Navy Yard it seemed like she had a job to do. Entering the ballpein she looked around at her co-worker faces, her friends that would protect her from McGee, Torez and landing on Gibbs she gave him a small smile before she was dragged into another case.

 **AN: so that is this story finished, I hope you enjoyed I might do a sequel later but more on the SHIELD side of it. What do you think? Check out my other stories thanks for reading Rubyrach.**


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